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The following R script simulates GWAS data for 5,000 SNPs across 22 chromosomes, injects association signals on chromosomes 6, 11, and 17, and produces a Manhattan plot with significance thresholds.
The ultimate objective of this chapter is to help users to connect input data to GWAS outputs to balance power and false positives, and connect GWAS outputs to the selection of candidate genes using LD extent.
To plot the variant with extreme P values (P < 1e-300), you can use scaled=True to create the plot with MLOG10P instead of raw P values. To calculate MLOG10P for extreme P values from BETA / SE or Z scores, you can use mysumstats.fill_data(to_fill=["MLOG10P"], extreme=True).
A Manhattan plot is a type of plot, usually used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values.